RBM12

RNA binding motif protein 12, the group of RNA binding motif containing

Basic information

Region (hg38): 20:35648924-35664956

Links

ENSG00000244462 ∙ NCBI:10137 ∙ OMIM:607179 ∙ HGNC:9898 ∙ Uniprot:Q9NTZ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schizophrenia 19	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	28628109

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBM12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM12 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	4	6
missense			43	5	1	49
nonsense						0
start loss						0
frameshift			1			1
inframe indel					2	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	7	7

Variants in RBM12

This is a list of pathogenic ClinVar variants found in the RBM12 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-35652547-T-C		not specified	Uncertain significance (May 30, 2024)
20-35652603-C-T		not specified	Uncertain significance (Feb 15, 2023)
20-35652648-T-C		not specified	Uncertain significance (Dec 22, 2023)
20-35652746-T-G		not specified	Uncertain significance (Mar 20, 2024)
20-35652764-T-C			Benign (Dec 31, 2019)
20-35652790-CA-C		Schizophrenia 19	Pathogenic (Aug 17, 2017)
20-35652813-G-T		not specified	Uncertain significance (Apr 27, 2022)
20-35652812-T-TGGGCCA		RBM12-related disorder	Benign (Dec 13, 2019)
20-35652818-A-G		RBM12-related disorder	Likely benign (Nov 26, 2019)
20-35652818-AGGGCCG-A		RBM12-related disorder	Benign (Oct 31, 2019)
20-35652823-C-T		not specified	Uncertain significance (Sep 15, 2021)
20-35652835-C-T		not specified	Uncertain significance (Dec 27, 2023)
20-35652914-C-T			Benign (Jul 05, 2018)
20-35652915-G-A		not specified	Uncertain significance (Sep 06, 2022)
20-35652922-C-T		not specified	Uncertain significance (Aug 30, 2021)
20-35652940-C-A		not specified	Uncertain significance (Dec 20, 2023)
20-35652946-C-A		Schizophrenia 19	Pathogenic (Aug 17, 2017)
20-35653063-T-A		not specified	Uncertain significance (Aug 12, 2021)
20-35653120-G-A			Uncertain significance (Feb 01, 2024)
20-35653261-G-A		not specified	Uncertain significance (Oct 10, 2023)
20-35653270-C-G		not specified	Uncertain significance (Jun 04, 2024)
20-35653299-G-A		not specified	Uncertain significance (Dec 22, 2023)
20-35653359-G-A			Likely benign (Dec 31, 2019)
20-35653362-T-C		not specified	Likely benign (Dec 12, 2022)
20-35653483-C-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM12	protein_coding	protein_coding	ENST00000374114	1	16032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00211	0.980	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	443	523	0.847	0.0000280	6087
Missense in Polyphen		67	105.27	0.63647		1367
Synonymous	-0.147	195	192	1.01	0.0000108	2015
Loss of Function	2.08	7	16.0	0.438	9.35e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000271
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000974	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Schizophrenia 19 (SCZD19) [MIM:617629]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:28628109}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.186

Intolerance Scores

• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.413
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rbm12
• Phenotype: growth/size/body region phenotype; embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Cellular component: nucleoplasm
• Molecular function: RNA binding;protein binding